A Ranking Model of Proximal and Structural Text RetrievalBased on Region Algebra Katsuya Masuda Department of Computer Science, Graduate School of Information Science and Technology, Uni
Trang 1A Ranking Model of Proximal and Structural Text Retrieval
Based on Region Algebra
Katsuya Masuda
Department of Computer Science, Graduate School of Information Science and Technology,
University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
kmasuda@is.s.u-tokyo.ac.jp
Abstract
This paper investigates an application of
the ranked region algebra to information
retrieval from large scale but unannotated
documents We automatically annotated
documents with document structure and
semantic tags by using taggers, and
re-trieve information by specifying
struc-ture represented by tags and words using
ranked region algebra We report in detail
what kind of data can be retrieved in the
experiments by this approach
1 Introduction
In the biomedical area, the number of papers is very
large and increases, as it is difficult to search the
in-formation Although keyword-based retrieval
sys-tems can be applied to a database of papers, users
may not get the information they want since the
re-lations between these keywords are not specified If
the document structures, such as “title”, “sentence”,
“author”, and relation between terms are tagged in
the texts, then the retrieval is improved by
ing such structures Models of the retrieval
specify-ing both structures and words are pursued by many
researchers (Chinenyanga and Kushmerick, 2001;
Wolff et al., 1999; Theobald and Weilkum, 2000;
Deutsch et al., 1998; Salminen and Tompa, 1994;
Clarke et al., 1995) However, these models are not
robust unlike keyword-based retrieval, that is, they
retrieve only the exact matches for queries
In the previous research (Masuda et al., 2003), we
proposed a new ranking model that enables proximal
and structural search for structured text This paper investigates an application of the ranked region al-gebra to information retrieval from large scale but unannotated documents We reports in detail what kind of data can be retrieved in the experiments Our approach is to annotate documents with document structures and semantic tags by taggers automati-cally, and to retrieve information by specifying both structures and words using ranked region algebra In this paper, we apply our approach to the OHSUMED test collection (Hersh et al., 1994), which is a public test collection for information retrieval in the field
of biomedical science but not tag-annotated We an-notate OHSUMED by various taggers and retrieve information from the tag-annotated corpus
We have implemented the ranking model in our retrieval engine, and had preliminary experiments to evaluate our model In the experiments, we used the GENIA corpus (Ohta et al., 2002) as a small but manually tag-annotated corpus, and OHSUMED as
a large but automatically tag-annotated corpus The experiments show that our model succeeded in re-trieving the relevant answers that an exact-matching model fails to retrieve because of lack of robustness, and the relevant answers that a non-structured model fails because of lack of structural specification We report how structural specification works and how it doesn’t work in the experiments with OHSUMED
Section 2 explains the region algebra In Section
3, we describe our ranking model for the structured query and texts In Section 4, we show the experi-mental results of this system
Trang 2Expression Description
q1¤ q2 G q1¤q2 = Γ({a|a ∈ G q1 ∧ ∃b ∈ G q2.(b < a)})
q16¤ q2 G q16¤q2 = Γ({a|a ∈ G q1∧ 6 ∃b ∈ G q2.(b < a)})
q1¢ q2 G q1¢q2 = Γ({a|a ∈ G q1 ∧ ∃b ∈ G q2.(a < b)})
q16¢ q2 G q16¢q2 = Γ({a|a ∈ G q1∧ 6 ∃b ∈ G q2.(a < b)})
q14 q2 G q14q2 = Γ({c|c < (−∞, ∞) ∧ ∃a ∈ G q1.∃b ∈ G q2.(a < c ∧ b < c)})
q15 q2 G q15q2 = Γ({c|c < (−∞, ∞) ∧ ∃a ∈ G q1.∃b ∈ G q2.(a < c ∨ b < c)})
q13 q2 G q13q2 = Γ({c|c = (p s , p 0
e ) where ∃(p s , p e ) ∈ G q1.∃(p 0
s , p 0
e ) ∈ G q2.(p e < p 0
s )})
Table 1: Operators of the Region algebra
!" # %$&'
Figure 1: Tree of the query ‘[book] ¤ ([title] ¤
“re-trieval”)’
2 Background: Region algebra
The region algebra (Salminen and Tompa, 1994;
Clarke et al., 1995; Jaakkola and Kilpelainen, 1999)
is a set of operators representing the relation
be-tween the extents (i.e regions in texts), where an
extent is represented by a pair of positions,
begin-ning and ending position Region algebra allows for
the specification of the structure of text
In this paper, we suppose the region algebra
pro-posed in (Clarke et al., 1995) It has seven
tors as shown in Table 1; four containment
opera-tors (¤, 6¤, ¢, 6¢) representing the containment
re-lation between the extents, two combination
oper-ators (4, 5) corresponding to “and” and “or”
op-erator of the boolean model, and ordering opop-erator
(3) representing the order of words or structures in
the texts A containment relation between the
ex-tents is represented as follows: e = (p s , p e) contains
e 0 = (p 0 s , p 0 e ) iff p s ≤ p 0 s ≤ p 0 e ≤ p e(we express this
relation as e = e 0) The result of retrieval is a set of
non-nested extents, that is defined by the following
function Γ over a set of extents S:
Γ(S) = {e|e ∈ S∧ 6 ∃e 0 ∈ S.(e 0 6= e ∧ e 0 < e)}
!" #%$& '
* )" #%$&+
/103254.6 79854;:<
=>8@? 7A8B4C:(<
Figure 2: Subqueries of the query ‘[book] ¤ ([title]
¤ “retrieval”)’
Intuitively, Γ(S) is an operation for finding the
shortest matching A set of non-nested extents
matching query q is expressed as G q For convenience of explanation, we represent a query as a tree structure as shown in Figure 1 (‘[x]’
is a abbreviation of ‘hxi 3 h/xi’) This query
rep-resents ‘Retrieve the books whose title has the word
“retrieval.” ’ The algorithm for finding an exact match of a query works efficiently The time complexity of the algorithm is linear to the size of a query and the size
of documents (Clarke et al., 1995)
3 A Ranking Model for Structured Queries and Texts
This section describes the definition of the relevance between a document and a structured query repre-sented by the region algebra The key idea is that a structured query is decomposed into subqueries, and the relevance of the whole query is represented as a vector of relevance measures of subqueries
Our model assigns a relevance measure of the
Trang 3q1 “hbooki” (1,1) (16,16) inverted list
Table 2: Extents that match each subquery in the extent (1, 15) and (16, 30)
hbooki htitlei ranked retrieval h/titlei hchapteri
htitlei tf and idf h/titlei ranked
retrieval h/chapteri h/booki hbooki htitlei structured
text h/titlei hchapteri htitlei search for
structured text h/titlei retrieval h/chapteri h/booki
Figure 3: An example text
structured query as a vector of relevance measures
of the subqueries In other words, the relevance
is defined by the number of portions matched with
subqueries in a document If an extent matches a
subquery of query q, the extent will be somewhat
relevant to q even when the extent does not exactly
match q Figure 2 shows an example of a query and
its subqueries In this example, even when an extent
does not match the whole query exactly, if the
ex-tent matches “retrieval” or ‘[title]¤“retrieval”’, the
extent is considered to be relevant to the query
Sub-queries are formally defined as follows
Definition 1 (Subquery) Let q be a given query
and n1, , n m be the nodes of q Subqueries
q1, , q m of q are the subtrees of q Each q i has
node n i as a root node.
When a relevance σ(q i , d) between a subquery
q i and a document d is given, the relevance of the
whole query is defined as follows
Definition 2 (Relevance of the whole query) Let q
be a given query, d be a document and q1, , q m be
subqueries of q The relevance vector Σ(q, d) of d is
defined as follows:
Σ(q, d) = hσ(q1, d), σ(q2, d), , σ(q m , d)i
A relevance of a subquery should be defined simi-larly to that of keyword-based queries in the tradi-tional ranked retrieval For example, TFIDF, which
is used in our experiments in Section 4, is the most simple and straightforward one, while other rele-vance measures recently proposed (Robertson and Walker, 2000; Fuhr, 1992) can be applied TF of a subquery is calculated using the number of extents matching the subquery, and IDF of a subquery is calculated using the number of documents includ-ing the extents matchinclud-ing the subquery When a text is given as Figure 3 and document collection is
{(1,15),(16,30)}, extents matching each subquery in
each document are shown in Table 2 TF and IDF are calculated using the number of extents matching subquery in Table 2
While we have defined a relevance of the struc-tured query as a vector, we need to arrange the doc-uments according to the relevance vectors In this paper, we first map a vector into a scalar value, and then sort the documents according to this scalar measure
Three methods are introduced for the mapping from the relevance vector to the scalar measure The first one simply works out the sum of the elements
of the relevance vector
Definition 3 (Simple Sum)
ρ sum (q, d) =
m
X
i=1
σ(q i , d)
The second appends a coefficient representing the
rareness of the structures When the query is A ¤ B
or A ¢ B, if the number of extents matching the query is close to the number of extents matching A,
matching the query does not seem to be very
impor-tant because it means that the extents that match A mostly match A ¤ B or A ¢ B The case of the other operators is the same as with ¤ and ¢.
Trang 4Num Query
1 ‘([cons] ¤ ([sem] ¤ “G#DNA domain or region”)) 4 (“in” 3 ([cons] ¤ ([sem] ¤ (“G#tissue” 5 “G#body part”))))’
2 ‘([event] ¤ ([obj] ¤ “gene”)) 4 (“in” 3 ([cons] ¤ ([sem] ¤ (“G#tissue” 5 “G#body part”))))’
3 ‘([event]¤([obj]3([sem]¤“G#DNA domain or region”)))4(“in”3([cons]¤([sem]¤(“G#tissue”5“G#body part”))))’
Table 3: Queries submitted in the experiments on the GENIA corpus
Definition 4 (Structure Coefficient) When the
op-erator op is 4, 5 or 3, the structure coefficient of
the query A op B is:
C(A) + C(B)
and when the operator op is ¤ or ¢, the structure
coefficient of the query A op B is:
C(A)
where A and B are the queries and C(A) is the
num-ber of extents that match A in the document
collec-tion.
The scalar measure ρ sc (q i , d) is then defined as
ρ sc (q, d) =
m
X
i=1
sc qi · σ(q i , d)
The third is a combination of the measure of the
query itself and the measure of the subqueries
Al-though we calculate the score of extents by
sub-queries instead of using only the whole query, the
score of subqueries can not be compared with the
score of other subqueries We assume normalized
weight of each subquery and interpolate the weight
of parent node and children nodes
Definition 5 (Interpolated Coefficient) The
inter-polated coefficient of the query q i is recursively
de-fined as follows:
ρ ic (q i , d) = λ · σ(q i , d) + (1 − λ)
P
ci ρ ic (q ci , d) l
where c i is the child of node n i , l is the number of
children of node n i , and 0 ≤ λ ≤ 1.
This formula means that the weight of each node is
defined by a weighted average of the weight of the
query and its subqueries When λ = 1, the weight
of a query is normalized weight of the query When
λ = 0, the weight of a query is calculated from the
weight of the subqueries, i.e the weight is
calcu-lated by only the weight of the words used in the
query
In this section, we show the results of our prelimi-nary experiments of text retrieval using our model
We used the GENIA corpus (Ohta et al., 2002) and the OHSUMED test collection (Hersh et al., 1994)
We compared three retrieval models, i) our model,
ii) exact matching of the region algebra (exact), and iii) not structured model (flat) The queries
submit-ted to our system are shown in Table 3 and 4 In
the flat model, the query was submitted as a query
composed of the words in the queries connected by
the “and” operator (4) For example, in the case of
Query 1, the query submitted to the system in the
flat model is ‘ “G#DNA domain or region” 4 “in”
4 “G#tissue” 4 “G#body part” ’ The system
out-put the ten results that had the highest relevance for each model
In the following experiments, we used a computer that had Pentium III 1.27GHz CPU, 4GB memory The system was implemented in C++ with Berkeley
DB library
4.1 GENIA corpus
The GENIA corpus is an XML document com-posed of paper abstracts in the field of biomedi-cal science The corpus consisted of 1,990 arti-cles, 873,087 words (including tags), and 16,391 sentences In the GENIA corpus, the document
structure was annotated by tags such as “harticlei” and “hsentencei”, technical terms were annotated by
“hconsi”, and events were annotated by “heventi”.
The queries in Table 3 are made by an expert in the field of biomedicine The document was “tence” in this experiments Query 1 retrieves sen-tences including a gene in a tissue Queries 2 and
3 retrieve sentences representing an event having a gene as an object and occurring in a tissue In Query
2, a gene was represented by the word “gene,” and in Query 3, a gene was represented by the annotation
“G#DNA domain or region.”
Trang 54 ‘ “postmenopausal” 4 ([neoplastic] ¤ (“breast” 3 “cancer”)) 4 ([therapeutic] ¤ (“replacement” 3 “therapy”)) ’
55 year old female, postmenopausal
does estrogen replacement therapy cause breast cancer
5 ‘ ([disease]¤(“copd”5(“chronic”3“obstructive”3“pulmonary”3“disease”)))4“theophylline”4([disease]¤“asthma”) ’
50 year old with copd
theophylline uses–chronic and acute asthma
6 ‘ ([neoplastic] ¤ (“lung” 3 “cancer”)) 4 ([therapeutic] ¤ (“radiation” 3 “therapy”)) ’
lung cancer
lung cancer, radiation therapy
7 ‘([disease]¤“pancytopenia”)4([neoplastic]¤(“acute”3“megakaryocytic”3“leukemia”))4(“treatment5“prognosis”)’
70 year old male who presented with pancytopenia
acute megakaryocytic leukemia, treatment and prognosis
8 ‘([disease]¤“hypercalcemia”)4([neoplastic]¤“carcinoma”)4(([therapeutic]¤“gallium”)5(“gallium”3“therapy”))’
57 year old male with hypercalcemia secondary to carcinoma
effectiveness of gallium therapy for hypercalcemia
9 ‘(“lupus”3“nephritis”)4(“thrombotic”3([disease]¤(“thrombocytopenic”3“purpura”))4(“management”5“diagnosis”)’
18 year old with lupus nephritis and thrombotic thrombocytopenic purpura
lupus nephritis, diagnosis and management
10 ‘ ([mesh] ¤ “treatment”) 4 ([disease] ¤ “endocarditis”) 4 ([sentence] ¤ (“oral” 3 “antibiotics”) ’
28 year old male with endocarditis
treatment of endocarditis with oral antibiotics
11 ‘ ([mesh] ¤ “female”) 4 ([disease] ¤ (“anorexia” 4 bulimia)) 4 ([disease] ¤ “complication”) ’
25 year old female with anorexia/bulimia
complications and management of anorexia and bulimia
12 ‘ ([disease] ¤ “diabete”) 4 ([disease] ¤ (“peripheral” 3 “neuropathy”)) 4 ([therapeutic] ¤ “pentoxifylline”) ’
50 year old diabetic with peripheral neuropathy
use of Trental for neuropathy, does it work?
13 ‘ (“cerebral” 3 “edema”) 4 ([disease] ¤ “infection”) 4 (“diagnosis” 5 ([therapeutic] ¤ “treatment”)) ’
22 year old with fever, leukocytosis, increased intracranial pressure, and central herniation
cerebral edema secondary to infection, diagnosis and treatment
14 ‘ ([mesh] ¤ “female”) 4 ([disease] ¤ (“urinary” 3 “tract” 3 “infection”)) 4 ([therapeutic] ¤ “treatment”) ’
23 year old woman dysuria
Urinary Tract Infection, criteria for treatment and admission
15 ‘ ([disease] ¤ (“chronic” 3 “fatigue” 3 “syndrome”)) 4 ([therapeutic] ¤ “treatment”) ’
chronic fatigue syndrome
chronic fatigue syndrome, management and treatment
Table 4: Queries submitted in the experiments on the OHSUMED test collection and original queries of OHSUMED The first line is a query submitted to the system, the second and third lines are the original query
of the OHSUMED test collection, the second is information of patient and the third is request information
For the exact model, ten results were selected
ran-domly from the exactly matched results if the
num-ber of results was more than ten The results are
blind tested, i.e., after we had the results for each
model, we shuffled these results randomly for each
query, and the shuffled results were judged by an
ex-pert in the field of biomedicine whether they were
relevant or not
Table 5 shows the number of the results that were
judged relevant in the top ten results The results
show that our model was superior to the exact and
flat models for all queries Compared to the exact
model, our model output more relevant documents,
since our model allows the partial matching of the
query, which shows the robustness of our model In
addition, our model gives a better result than the flat
model, which means that the structural specification
of the query was effective for finding the relevant documents
Comparing our models, the number of relevant
re-sults using ρ sc was the same as that of ρ sum The
re-sults using ρ ic varied between the results of the flat model and the results of the exact model depending
on the value of λ.
4.2 OHSUMED test collection
The OHSUMED test collection is a document set composed of paper abstracts in the field of
Trang 6biomed-Query our model exact flat
(λ = 0.25) (λ = 0.5) (λ = 0.75)
Table 5: (The number of relevant results) / (the number of all results) in top 10 results on the GENIA corpus
(λ = 0.25) (λ = 0.5) (λ = 0.75)
Table 6: (The number of relevant results) / (the number of all results) in top 10 judged results on the
OHSUMED test collection (“all results” are relevance-judged results in the exact model)
ical science The collection has a query set and a
list of relevant documents for each query From 50
to 300 documents are judged whether or not
rele-vant to each query The query consisted of patient
information and information request We used
ti-tle, abstract, and human-assigned MeSH term fields
of documents in the experiments Since the
origi-nal OHSUMED is not annotated with tags, we
an-notated it with tags representing document
struc-tures such as “harticlei” and “hsentencei”, and
an-notated technical terms with tags such as “hdiseasei”
and “htherapeutici” by longest matching of terms of
Unified Medical Language System (UMLS) In the
OHSUMED, relations between technical terms such
as events were not annotated unlike the GENIA
cor-pus The collection consisted of 348,566 articles,
78,207,514 words (including tags), and 1,731,953
sentences
12 of 106 queries of OHSUMED are converted
into structured queries of Region Algebra by an ex-pert in the field of biomedicine These queries are shown in Table 4, and submitted to the system The document was “article” in this experiments For the
exact model, all exact matches of the whole query
were judged Since there are documents that are not judged whether or not relevant to the query in the OHSUMED, we picked up only the documents that are judged
Table 6 shows the number of relevant results in top ten results The results show that our model
suc-ceeded in finding the relevant results that the exact model could not find, and was superior to the flat
model for Query 4, 5, and 6 However, our model
was inferior to the flat model for Query 14 and 15.
Comparing our models, the number of relevant
results using ρ sc and ρ ic was lower than that using
ρ sum
Trang 7Query our model exact
Table 7: The retrieval time (sec.) on GENIA corpus
Query our model exact
4 25.13 s 2.17 s
5 24.77 s 3.13 s
6 23.84 s 2.18 s
7 24.00 s 2.70 s
8 27.62 s 3.50 s
9 20.62 s 2.22 s
10 30.72 s 7.60 s
11 25.88 s 4.59 s
12 25.44 s 4.28 s
13 21.94 s 3.30 s
14 28.44 s 4.38 s
15 20.36 s 3.15 s
Table 8: The retrieval time (sec.) on OHSUMED
test collection
4.3 Discussion
In the experiments on OHSUMED, the number of
relevant documents of our model were less than that
of the flat model in some queries We think this is
because i) specifying structures was not effective, ii)
weighting subqueries didn’t work, iii) MeSH terms
embedded in the documents are effective for the flat
model and not effective for our model, iv) or there
are many documents that our system found relevant
but were not judged since the OHSUMED test
col-lection was made using keyword-based retrieval
As for i), structural specification in the queries
is not well-written because the exact model failed
to achieve high precision and its coverage is very
low We used only tags specifying technical terms as
structures in the experiments on OHSUMED This
structure was not so effective because these tags are
annotated by longest match of terms We need to
use the tags representing relations between
techni-cal terms to improve the results Moreover,
struc-tured query used in the experiments may not specify
the request information exactly Therefore we think
converting queries written by natural language into the appropriate structured queries is important, and lead to the question answering using variously tag-annotated texts
As for ii), we think the weighting didn’t work because we simply use frequency of subqueries for weighting To improve the weighting, we have to assign high weight to the structure concerned with user’s intention, that are written in the request in-formation This is shown in the results of Query
9 In Query 9, relevant documents were not
re-trieved except the model using ρ ic, because although the request information was information concerned
“lupus nephritis”, the weight concerned with “lu-pus nephritis” was smaller than that concerned with
“thrombotic” and “thrombocytopenic purpura” in
the models except ρ ic Because the structures con-cerning with user’s intention did not match the most weighted structures in the model, the relevant docu-ments were not retrieved
As for iii), MeSH terms are human-assigned key-words for each documents, and no relation exists across a boundary of each MeSH terms in the
flat model, these MeSH term will improve the re-sults However, in our model, the structure
some-times matches that are not expected For example,
In the case of Query 14, the subquery ‘ “chronic”
3 “fatigue” 3 “syndrome” ’ matched in the field of
MeSH term across a boundary of terms when the MeSH term field was text such as “Affective Disor-ders/*CO; Chronic Disease; Fatigue/*PX; Human;
Syndrome ” because the operator 3 has no
limita-tion of distance
As for iv), the OHSUMED test collection was constructed by attaching the relevance judgement to the documents retrieved by keyword-based retrieval
To show the effectiveness of structured retrieval more clearly, we need test collection with (struc-tured) query and lists of relevant documents, and the tag-annotated documents, for example, tags repre-senting the relation between the technical terms such
as “event”, or taggers that can annotate such tags Table 7 and 8 show that the retrieval time in-creases corresponding to the size of the document collection The system is efficient enough for infor-mation retrieval for a rather small document set like GENIA corpus To apply to the huge databases such
as Web-based applications, we might require a
Trang 8con-stant time algorithm, which should be the subject of
future research
5 Conclusions and Future work
We proposed an approach to retrieve information
from documents which are not annotated with any
tags We annotated documents with document
struc-tures and semantic tags by taggers, and retrieved
information by using ranked region algebra We
showed what kind of data can be retrieved from
doc-uments in the experiments
In the discussion, we showed several points about
the ranked retrieval for structured texts Our future
work is to improve a model, corpus etc to improve
the ranked retrieval for structured texts
Acknowledgments
I am grateful to my supervisor, Jun’ichi Tsujii, for
his support and many valuable advices I also thank
to Takashi Ninomiya, Yusuke Miyao for their
valu-able advices, Yoshimasa Tsuruoka for providing me
with a tagger, Tomoko Ohta for making queries, and
anonymous reviewers for their helpful comments
This work is a part of the Kototoi project1supported
by CREST of JST (Japan Science and Technology
Corporation)
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...3 A Ranking Model for Structured Queries and Texts
This section describes the definition of the relevance between a document and a structured query repre-sented by the region algebra... results of the flat model and the results of the exact model depending
on the value of λ.
4.2 OHSUMED test collection
The OHSUMED test collection is a document... of text retrieval using our model
We used the GENIA corpus (Ohta et al., 2002) and the OHSUMED test collection (Hersh et al., 1994)
We compared three retrieval models, i) our model,